Journal: NAR Genomics and Bioinformatics

Article Title: Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases

doi: 10.1093/nargab/lqag053

Figure Lengend Snippet: Comparisons of genome coverage and variant calling. ( a ) Differential coverage across the top 15 most variable genome stratifications. Difference measure relative to mean autosomal coverage for the dataset. ( b ) Candidate small variant calls filtered out by DeepVariant across coverage from 10× to 50×. ( c ) F1-score for variant calling for SNPs and INDELs at different levels of genome coverage, as reported by hap.py. PacBio HiFi DeepVariant calls were used as the truth set. Cell line REH was omitted as HiFi coverage was insufficient. ( d ) Relative F1-score for SNPs and INDELs combined comparing AVITI to NovaSeq X Plus across GIAB stratifications (v3.5). The plot shows the top 15 most variable genome stratifications, split by mean overall coverage range. Bars show the mean difference across the subsampled datasets. TR = tandem repeat, HP = homopolymer, Imp. HP = imperfect HP, N-mer = TR composed of N bp repeated elements.

Article Snippet: PacBio HiFi sequencing libraries for MM1S, OPM2, and KMS12BM were prepared using the same high-molecular-weight gDNA source as the short read libraries and the SMRTbell prep kit 3.0 (Pacific Biosciences, #102-141-700).

Techniques: Variant Assay

Journal: bioRxiv

Article Title: From external-input sensitivity to resident persistence: community assembly in a sink p-trap model

doi: 10.64898/2026.05.13.724980

Figure Lengend Snippet: The dominant compositional gradient was organized by time in both amplicon and metagenomic profiles. (A) PC1 versus time in the full-length 16S dataset. (B) PC1 versus time in the shotgun metagenomic dataset.

Article Snippet: Raw PacBio HiFi full-length 16S reads were processed into ASV tables using the Pacific Biosciences HiFi 16S workflow , which implements DADA2-based denoising .

Techniques: Amplification